GSM5639714: H1993 IFNγ IRF1 1; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
IRF1
Cell type
Cell type Class
Lung
Cell type
NCI-H1993
Primary Tissue
Lung
Site of Extraction
Lymph Node
Tissue Diagnosis
Carcinoma Non-Small Cell
Attributes by original data submitter
Sample
source_name
ATCC
cell line
NCI-H1993
tissue
Lung
antibody
IRF1
Sex
female
age
47 years adult
source
Non-Small cell lung cancer
treatment
IFNg
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP, cells were grown and fixed with 1% methanol-free formaldehyde (Thermo Scientific) for 10 min and quenched by 125 mmol/L glycine for 15 min at room temperature and, after that, washed with ice-cold PBS twice. Then, the cells were centrifuged (200g at 4°C) for 5 min and the pellet resuspended in 1 mL of lysis buffer (10 mmol/L Tris-HCl, 10 mmol/L NaCl, 0.5% NP-40) containing a Halt Protease & Phosphatase Inhibitor Cocktail (Thermo Scientific; Ref: 78440) and kept rotating for 30 min at 4°C. After centrifugation, the pellet was then resuspended in 1 mL of nuclear lysis buffer (1% SDS, 10 mmol/L EDTA, 50 mmol/L Tris-HCl pH 8.0, protease inhibitor) and kept at 4°C for 60 min. After another centrifugation, the lysate was sonicated with a Covaris M220 instrument to yield chromatin fragments of a size of 0.25–1.00 kb on average, then frozen at -20ºC for 30 min, thawed on ice and centrifuged at 2,500 g. For each ChIP reaction, 60 μL of Magna ChIP™ Protein A+G Magnetic Beads (Merck Millipore. Cat: #16-663) was used in accordance with the manufacturer's protocol. Before addition of the sheared chromatin to the beads, Triton X-100 and Na-deoxycholate was added to a final concentration of 10% each. 1% of the chromatin volume was used for input. At least two independent ChIP experiments were performed. Immunoprecipitated chromatin was deep sequenced in the Genomics Unit of the Centre for Genomic Regulation (CRG, Barcelona, Spain) using the Illumina HiSeq 2500 system (Illumina). Briefly, library preparation included end-repair, generation of dA overhangs, adapter ligation, size selection and removal of non-ligated adapters by agarose gene electrophoresis and amplification (18 cycles) before loading the samples into the sequencer.